How do crystals get their color? The presence of different chemicals causes the variety of colors to different gemstones. Many gems are simply quartz crystals colored by the environments to which they are exposed. Amethyst gets its color from iron found at specific points in the crystalline structure. Topaz is an aluminium silicate - it comes in many colors due to the presence of different chemicals. The color of any compound (whether or not it is a crystal) depends on how the atoms and or molecules absorb light. Normally white light (what comes out of light bulbs) is considered to have all wavelengths (colors) of light in it. If you pass a white light through a colored compound some of the light is absorbed (we don't see the color which is absorbed, but we see the rest of the light) as it is reflected off the surface. This gives rise to the idea of "Complementary Colors". If a compound absorbs light of a certain color the compound appears to be the complimentary color. Here is a table of colors and their compliments:
 
Color Compliment Wavelength
(of color nm)

violet green-yellow    400-424
blue yellow                424-491
green red                  491-570
yellow blue                570-585
orange green-blue    585-647
red green                   647-700

So if you have a crystal which absorbs red light, it will appear green and if the crystal absorbs green light, it will appear red.